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Question: GEOquery error in downloading SOFT files
1
gravatar for hzc363
12 months ago by
hzc36320
hzc36320 wrote:

I try to download the soft file of a GSM from GEO:

getGEO("GSM998923",destdir='Data')

I get the following error:

Error in download.file(myurl, destfile, mode = mode, quiet = TRUE, method = getOption("download.file.method.GEOquery")) : 
  cannot open URL 'http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?targ=self&acc=GSM998923&form=text&view=full'

 

I then tried to see if it is an internet problem, so I copied the url in the error message and did this:

url="http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?targ=self&acc=GSM998923&form=text&view=full"

download.file(url,destdir="Data")

This time it works. The content in the url is downloaded without problem. 

So my question is, why the getGEO function give me the error and how can I fix it?


I am using "R version 3.3.1 (2016-06-21)" and GEOquery 2.40.0

ADD COMMENTlink modified 12 months ago • written 12 months ago by hzc36320
0
gravatar for Sean Davis
12 months ago by
Sean Davis21k
United States
Sean Davis21k wrote:

An upgrade to GEOquery 2.40 will likely fix the problem.  NCBI has moved away from using "http" in favor of "https", so you'll need to update GEOquery to address that issue.  Sorry for the inconvenience!

 

ADD COMMENTlink written 12 months ago by Sean Davis21k
1

upgrade works! Thanks. 

ADD REPLYlink written 12 months ago by hzc36320
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